Use of algorithms for semi-automatic quantification of pulmonary fibrosis and emphysema

Obtaining a semi-automatic quantification of pathologies found in the lung, through images of high resolution computed tomography (HRCT), is of great importance to aid in medical diagnosis. Paraccocidioidomycosis (PCM) is a systemic disease that affects the lung and even after effective treatment leaves sequels such as pulmonary fibrosis and emphysema. It is very important to the area of tropical diseases that the lung injury be quantified more accurately. In this stud, we propose the development of algorithms in computational environment Matlab® able to objectively quantify lung diseases such as fibrosis and emphysema. The program consists in selecting the region of interest (ROI), and through the use of density masks and filters, obtaining the lesion area quantification in relation to the healthy area of the lung. The proposed method was tested on 15 exams of HRCT of patients with confirmed PCM. To prove the validity and effectiveness of the method, we used a virtual phantom, also developed in this research. © 2013 Springer-Verlag.

Report on the production of trade statistics in the Caribbean region

Includes bibliography

Entomofauna associada a goiabeira Psidium guajava L. em pomares experimentais comerciais em Vista Alegre do Alto – SP e semi-orgânicos em Pindorama – SP

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Identification of human T-cell lymphotropic virus infection in a semi-isolated Afro-Brazilian quilombo located in the Marajó Island (Pará, Brazil)

ABSTRACT: Antibodies to human T-cell lymphotropic virus-1 and 2 (HTLV-1 and 2) were tested in 259 inhabitants (98 males and 161 females) of four villages of the Marajó Island (Pará, Brazil) using enzyme immunoassays (ELISA and Western blot). Types and subtypes of HTLV were determined by nested polymerase chain reaction (PCR) targeting the pX, env and 5´LTR regions. HTLV-1 infection was detected in Santana do Arari (2.06%) and Ponta de Pedras (1%). HTLV-2 was detected only in Santana do Arari (1.06%). Sequencing of the 5´LTR region of HTLV-1 and the phylogenetic analysis identified the virus as a member of the Cosmopolitan Group, subgroup Transcontinental. Santana do Arari is an Afro-Brazilian community and the current results represent the first report of HTLV-1 infection in a mocambo located in the Brazilian Amazon region.

Região do espaço que mais influencia em medidas eletromagnéticas no domínio da frequência: caso de uma linha de corrente sobre um semi-espaço condutor

Localizar em subsuperfície a região que mais influencia nas medidas obtidas na superfície da Terra é um problema de grande relevância em qualquer área da Geofísica. Neste trabalho, é feito um estudo sobre a localização dessa região, denominada aqui zona principal, para métodos eletromagnéticos no domínio da freqüência, utilizando-se como fonte uma linha de corrente na superfície de um semi-espaço condutor. No modelo estudado, tem-se, no interior desse semi-espaço, uma heterogeneidade na forma de camada infinita, ou de prisma com seção reta quadrada e comprimento infinito, na direção da linha de corrente. A diferença entre a medida obtida sobre o semi-espaço contendo a heterogeneidade e aquela obtida sobre o semi-espaço homogêneo, depende, entre outros parâmetros, da localização da heterogeneidade em relação ao sistema transmissor-receptor. Portanto, mantidos constantes os demais parâmetros, existirá uma posição da heterogeneidade em que sua influência é máxima nas medidas obtidas. Como esta posição é dependente do contraste de condutividade, das dimensões da heterogeneidade e da freqüência da corrente no transmissor, fica caracterizada uma região e não apenas uma única posição em que a heterogeneidade produzirá a máxima influência nas medidas. Esta região foi denominada zona principal. Identificada a zona principal, torna-se possível localizar com precisão os corpos que, em subsuperfície, provocam as anomalias observadas. Trata-se geralmente de corpos condutores de interesse para algum fim determinado. A localização desses corpos na prospecção, além de facilitar a exploração, reduz os custos de produção. Para localizar a zona principal, foi definida uma função Detetabilidade (∆), capaz de medir a influência da heterogeneidade nas medidas. A função ∆ foi calculada para amplitude e fase das componentes tangencial (H_x) e normal (H_z) à superfície terrestre do campo magnético medido no receptor. Estudando os extremos da função ∆ sob variações de condutividade, tamanho e profundidade da heterogeneidade, em modelos unidimensionais e bidimensionais, foram obtidas as dimensões da zona principal, tanto lateralmente como em profundidade. Os campos eletromagnéticos em modelos unidimensionais foram obtidos de uma forma híbrida, resolvendo numericamente as integrais obtidas da formulação analítica. Para modelos bidimensionais, a solução foi obtida através da técnica de elementos finitos. Os valores máximos da função ∆, calculada para amplitude de H_x, mostraram-se os mais indicados para localizar a zona principal. A localização feita através desta grandeza apresentou-se mais estável do que através das demais, sob variação das propriedades físicas e dimensões geométricas, tanto dos modelos unidimensionais como dos bidimensionais. No caso da heterogeneidade condutora ser uma camada horizontal infinita (caso 1D), a profundidade do plano central dessa camada vem dada pela relação p_o = 0,17 δ_o, onde p_o é essa profundidade e δ_o o "skin depth" da onda plana (em um meio homogêneo de condutividade igual à do meio encaixante (σ₁) e a freqüência dada pelo valor de w em que ocorre o máximo de ∆ calculada para a amplitude de H_x). No caso de uma heterogeneidade bidimensional (caso 2D), as coordenadas do eixo central da zona principal vem dadas por d_o = 0,77 r₀ (sendo d_o a distância horizontal do eixo à fonte transmissora) e p_o = 0,36 δ_o (sendo p_o a profundidade do eixo central da zona principal), onde r₀ é a distância transmissor-receptor e δ_o o "skin depth" da onda plana, nas mesmas condições já estipuladas no caso 1D. Conhecendo-se os valores de r₀ e δ_o para os quais ocorre o máximo de ∆, calculado para a amplitude de H_x, pode-se determinar (d_o, p_o). Para localizar a zona principal (ou, equivalentemente, uma zona condutora anômala em subsuperfície), sugere-se um método que consiste em associar cada valor da função ∆ da amplitude de H_x a um ponto (d, p), gerado através das relações d = 0,77 r e p = 0,36 δ, para cada w, em todo o espectro de freqüências das medidas, em um dado conjunto de configurações transmissor-receptor. São, então, traçadas curvas de contorno com os isovalores de ∆ que vão convergir, na medida em que o valor de ∆ se aproxima do máximo, sobre a localização e as dimensões geométricas aproximadas da heterogeneidade (zona principal).

Multiple Determinants of Anuran Richness and Occurrence in an Agricultural Region in South-Eastern Brazil

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Absence of detection of xanthomonas axonopodis pv. malvacearum in cotton seeds used in the Northeast Region of Mato Grosso do Sul in a three-based crop season study

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Search for exclusive or semi-exclusive gamma gamma production and observation of exclusive and semi-exclusive e(+)e(-) production in pp collisions at root s=7 TeV

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Trichomes related to an unusual method of water retention and protection of the stem apex in an arid zone perennial species

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Metals and semi-metals in street soils of So Paulo city, Brazil

So Paulo is the largest city in Brazil and South America with about 20 million inhabitants in the metropolitan area, more than nine million motor vehicles and intense industrial activity, which are responsible for increasing pollution in the region. Nevertheless, little is known concerning metal and semi-metal content in the soils of this metropolitan region. This type of information could be extremely useful as a fingerprint of environmental pollution. The present study determined the elements As, Ba, Co, Cr, Sb, and Zn concentrations in soils adjacent to avenues of highly dense traffic in So Paulo city to assess their levels and possible sources. The analytical technique employed was Instrumental neutron activation analysis. The results showed, except for Co, concentration levels higher than the reference values for soils of So Paulo, according to the Environmental Protection Agency of the State of So Paulo guidelines. When compared to similar studies in other cities around the world, So Paulo soils presented higher levels, probably due to its high density traffic and industrial activity. The concentrations obtained for As and Cr indicate anthropogenic origin. The high levels of the traffic-related elements Ba, Sb, and Zn in soils nearby high density traffic avenues indicate they may originate from vehicular exhausts.

Experimental study on vortex-induced motions of a semi-submersible platform with four square columns, Part I: Effects of current incidence angle and hull appendages

An experimental study on Vortex-Induced Motion (VIM) of the semi-submersible platform concept with four square columns is presented. Model tests were carried out to check the influence of different headings and hull appendages (riser supports located at the pontoons; fairleads and the mooring stretches located vertically at the external column faces; and hard pipes located vertically at the internal column faces). The results comprise in-line, transverse and yaw motions, as well as combined motions in the XY plane, drag and lift forces and spectral analysis. The main results showed that VIM in the transverse direction occurred in a range of reduced velocity 4.0 up to 14.0 with amplitude peaks around reduced velocities around 7.0 and 8.0. The largest transverse amplitudes obtained were around 40% of the column width for 30 degrees and 45 degrees incidences. Another important result observed was a considerable yaw motion oscillation, in which a synchronization region could be identified as a resonance phenomenon. The largest yaw motions were verified for the 0 degrees incidence and the maxima amplitudes around 4.5 degrees. The hull appendages located at columns had the greatest influence on the VIM response of the semi-submersible. (C) 2012 Elsevier Ltd. All rights reserved.

Serological detection of Plasmodium vivax malaria using recombinant proteins corresponding to the 19-kDa C-terminal region of the merozoite surface protein-1

Abstract Background Serological tests to detect antibodies specific to Plasmodium vivax could be a valuable tool for epidemiological studies, for screening blood donors in areas where the malaria is not endemic and for diagnosis of infected individuals. Because P. vivax cannot be easily obtained in vitro, ELISA assays using total or semi-purified antigens are rarely used. Based on this limitation, we tested whether recombinant proteins representing the 19 kDa C-terminal region of the merozoite surface protein-1 of P. vivax (MSP119) could be useful for serological detection of malaria infection. Methods Three purified recombinant proteins produced in Escherichia coli (GST-MSP119, His6-MSP119 and His6-MSP119-PADRE) and one in Pichia pastoris (yMSP119-PADRE) were compared for their ability to bind to IgG antibodies of individuals with patent P. vivax infection. The method was tested with 200 serum samples collected from individuals living in the north of Brazil in areas endemic for malaria, 53 serum samples from individuals exposed to Plasmodium falciparum infection and 177 serum samples from individuals never exposed to malaria. Results Overall, the sensitivity of the ELISA assessed with sera from naturally infected individuals was 95%. The proportion of serum samples that reacted with recombinant proteins GST-MSP119, His6-MSP119, His6-MSP119-PADRE and yMSP119-PADRE was 90%, 93.5%, 93.5% and 93.5%, respectively. The specificity values of the ELISA determined with sera from healthy individuals and from individuals with other infectious diseases were 98.3% (GST-MSP119), 97.7% (His6-MSP119 and His6-MSP119-PADRE) or 100% (yMSP119-PADRE). Conclusions Our study demonstrated that for the Brazilian population, an ELISA using a recombinant protein of the MSP119 can be used as the basis for the development of a valuable serological assay for the detection of P. vivax malaria.

Identification of SL addition trans-splicing acceptor sites in the internal transcribed spacer I region of pre-rRNA in Leishmania (Leishmania) amazonensis

Trypanosomatidae is a family of early branching eukaryotes harbouring a distinctive repertoire of gene expression strategies. Functional mature messenger RNA is generated via the trans-splicing and polyadenylation processing of constitutively transcribed polycistronic units. Recently, trans-splicing of pre-small subunit ribosomal RNA in the 5' external transcribed spacer region and of precursor tRNAsec have been described. Here, we used a previously validated semi-nested reverse transcription-polymerase chain reaction strategy to investigate internal transcribed spacer (ITS) I acceptor sites in total RNA from Leishmania (Leishmania) amazonensis. Two distinct spliced leader-containing RNAs were detected indicating that trans-splicing reactions occur at two AG acceptor sites mapped in this ITS region. These data provide further evidence of the wide spectrum of RNA molecules that act as trans-splicing acceptors in trypanosomatids.

Lesion detection and classification in breast cancer: evaluation of approaches based on morphological features, tracer kinetic modelling and semi-quantitative parameters in MR functional imaging (DCE-MRI)

The diagnosis, grading and classification of tumours has benefited considerably from the development of DCE-MRI which is now essential to the adequate clinical management of many tumour types due to its capability in detecting active angiogenesis. Several strategies have been proposed for DCE-MRI evaluation. Visual inspection of contrast agent concentration curves vs time is a very simple yet operator dependent procedure, therefore more objective approaches have been developed in order to facilitate comparison between studies. In so called model free approaches, descriptive or heuristic information extracted from time series raw data have been used for tissue classification. The main issue concerning these schemes is that they have not a direct interpretation in terms of physiological properties of the tissues. On the other hand, model based investigations typically involve compartmental tracer kinetic modelling and pixel-by-pixel estimation of kinetic parameters via non-linear regression applied on region of interests opportunely selected by the physician. This approach has the advantage to provide parameters directly related to the pathophysiological properties of the tissue such as vessel permeability, local regional blood flow, extraction fraction, concentration gradient between plasma and extravascular-extracellular space. Anyway, nonlinear modelling is computational demanding and the accuracy of the estimates can be affected by the signal-to-noise ratio and by the initial solutions. The principal aim of this thesis is investigate the use of semi-quantitative and quantitative parameters for segmentation and classification of breast lesion. The objectives can be subdivided as follow: describe the principal techniques to evaluate time intensity curve in DCE-MRI with focus on kinetic model proposed in literature; to evaluate the influence in parametrization choice for a classic bi-compartmental kinetic models; to evaluate the performance of a method for simultaneous tracer kinetic modelling and pixel classification; to evaluate performance of machine learning techniques training for segmentation and classification of breast lesion.

Numerical and semi-analytical models of sliding masses: application to the 1783 Scilla tsunamigenic landslide

The Scilla rock avalanche occurred on 6 February 1783 along the coast of the Calabria region (southern Italy), close to the Messina Strait. It was triggered by a mainshock of the Terremoto delle Calabrie seismic sequence, and it induced a tsunami wave responsible for more than 1500 casualties along the neighboring Marina Grande beach. The main goal of this work is the application of semi-analtycal and numerical models to simulate this event. The first one is a MATLAB code expressly created for this work that solves the equations of motion for sliding particles on a two-dimensional surface through a fourth-order Runge-Kutta method. The second one is a code developed by the Tsunami Research Team of the Department of Physics and Astronomy (DIFA) of the Bologna University that describes a slide as a chain of blocks able to interact while sliding down over a slope and adopts a Lagrangian point of view. A wide description of landslide phenomena and in particular of landslides induced by earthquakes and with tsunamigenic potential is proposed in the first part of the work. Subsequently, the physical and mathematical background is presented; in particular, a detailed study on derivatives discratization is provided. Later on, a description of the dynamics of a point-mass sliding on a surface is proposed together with several applications of numerical and analytical models over ideal topographies. In the last part, the dynamics of points sliding on a surface and interacting with each other is proposed. Similarly, different application on an ideal topography are shown. Finally, the applications on the 1783 Scilla event are shown and discussed.